Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 196 of 208
Found at i:59706958 original size:3 final size:3
Alignment explanation
Indices: 59706952--59706978 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
59706942 TCTTGTTGTA
59706952 ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG
59706979 GCGGCGGCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:59717390 original size:5 final size:5
Alignment explanation
Indices: 59717380--59717416 Score: 56
Period size: 5 Copynumber: 7.0 Consensus size: 5
59717370 CAACAGCAGA
59717380 AGATG AGATG AGATG AGATG AGATG AGGATTG AGATG
1 AGATG AGATG AGATG AGATG AGATG A-GA-TG AGATG
59717417 GCCCACTAAC
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 23 0.77
6 4 0.13
7 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.41, T:0.22
Consensus pattern (5 bp):
AGATG
Found at i:59723389 original size:7 final size:7
Alignment explanation
Indices: 59723377--59723401 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
59723367 AAAGTATTTT
59723377 AAAAATA
1 AAAAATA
59723384 AAAAATA
1 AAAAATA
59723391 AAAAATA
1 AAAAATA
59723398 AAAA
1 AAAA
59723402 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:59726867 original size:28 final size:28
Alignment explanation
Indices: 59726827--59726884 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
59726817 CTCATATGAG
59726827 AAGAACATTAGATGCTTAAGTTCATTCC
1 AAGAACATTAGATGCTTAAGTTCATTCC
59726855 AAGAACATTAGATGCTTAAGTTCATTCC
1 AAGAACATTAGATGCTTAAGTTCATTCC
59726883 AA
1 AA
59726885 CCTACAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (28 bp):
AAGAACATTAGATGCTTAAGTTCATTCC
Found at i:59729119 original size:23 final size:23
Alignment explanation
Indices: 59729093--59729140 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
59729083 GGAAAATGTA
*
59729093 AAATTAATCATTATATATTAAAT
1 AAATTAATCATTATACATTAAAT
* *
59729116 AAATTCATCCTTATACATTAAAT
1 AAATTAATCATTATACATTAAAT
59729139 AA
1 AA
59729141 CACACCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATTAATCATTATACATTAAAT
Found at i:59736860 original size:21 final size:18
Alignment explanation
Indices: 59736821--59736861 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 18
59736811 ATAACAAAGG
59736821 AAATAAAAAAAATTTTAA
1 AAATAAAAAAAATTTTAA
59736839 AAATAAAGAATAAATATTTAA
1 AAATAAA-AA-AAAT-TTTAA
59736860 AA
1 AA
59736862 GAATAACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 2 0.10
20 4 0.20
21 7 0.35
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAATAAAAAAAATTTTAA
Found at i:59737042 original size:30 final size:30
Alignment explanation
Indices: 59737008--59737067 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
59736998 TCTAATCAAC
*
59737008 CCTCTAAGAAATAATCTTTGGCAAATTGAA
1 CCTCTAAGAAATAATATTTGGCAAATTGAA
59737038 CCTCTAAGAAATAATATTTGGCAAATTGAA
1 CCTCTAAGAAATAATATTTGGCAAATTGAA
59737068 ATGTGAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.13, T:0.30
Consensus pattern (30 bp):
CCTCTAAGAAATAATATTTGGCAAATTGAA
Found at i:59740520 original size:42 final size:42
Alignment explanation
Indices: 59740461--59740546 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
59740451 TATAATAAAA
59740461 GAATGAATCAAAACTCAATTCGCATCCTTCATTATAGACTAG
1 GAATGAATCAAAACTCAATTCGCATCCTTCATTATAGACTAG
59740503 GAATGAATCAAAACTCAATTCGCATCCTTCATTATAGACTAG
1 GAATGAATCAAAACTCAATTCGCATCCTTCATTATAGACTAG
59740545 GA
1 GA
59740547 TCATGAATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (42 bp):
GAATGAATCAAAACTCAATTCGCATCCTTCATTATAGACTAG
Found at i:59748178 original size:2 final size:2
Alignment explanation
Indices: 59748173--59748207 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
59748163 AATATAAAAG
*
59748173 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59748208 AATTATAAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59748469 original size:25 final size:26
Alignment explanation
Indices: 59748423--59748479 Score: 69
Period size: 29 Copynumber: 2.1 Consensus size: 26
59748413 ATTCATAAAA
59748423 ATTAAAAACAATATGTACGTATATAT
1 ATTAAAAACAATATGTACGTATATAT
* *
59748449 ATTAAAAAAAATCGTATGTATGTATATAT
1 ATTAAAAACAA---TATGTACGTATATAT
59748478 AT
1 AT
59748480 ATATAGGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 10 0.38
29 16 0.62
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.37
Consensus pattern (26 bp):
ATTAAAAACAATATGTACGTATATAT
Found at i:59748731 original size:3 final size:3
Alignment explanation
Indices: 59748717--59748796 Score: 92
Period size: 3 Copynumber: 26.7 Consensus size: 3
59748707 CAAATAAAAC
* * *
59748717 TAA TAA TGA TAA TAAA TAA TAA TAA TAA TAA TGA TAA TAA TAA CAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
59748763 TAA TAA TAA TAA TAA -AA CTAA T-T TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TA
59748797 GAAATAACAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
2 3 0.05
3 57 0.88
4 5 0.08
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:59750451 original size:50 final size:48
Alignment explanation
Indices: 59750397--59750622 Score: 166
Period size: 50 Copynumber: 4.5 Consensus size: 48
59750387 CGAAAAAAGC
*
59750397 AAGATTCGCCGTTGTGGCTTCAATCTGTTCTGTTGCACTGCCTGGAATGT
1 AAGATTCGCCGTTGTGGCTTCAATCT-TTCTGTTGCACTGCATGGAA-GT
* * * * *
59750447 AAGATTCACCGTTGTGGCTTCAATCTTT-TAAATTACAATGTCAGGGAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCTTTCT--GTTGCACTG-CATGGAAGT
* * * * * *
59750497 GAGATTCGCCGTCGTCGCTTCAATCTATTCCGCTGCACTGCTTGGAAAGT
1 AAGATTCGCCGTTGTGGCTTCAATCT-TTCTGTTGCACTGCATGG-AAGT
* * * * * ** *
59750547 AAGATTCGCCATTGTAGCTTCAATCTTTCTAATTGTAATGTCGGGGAAGC
1 AAGATTCGCCGTTGTGGCTTCAATCTTTCT-GTTGCACTG-CATGGAAGT
* *
59750597 AAGATTCGCCATTGTGACTTCAATCT
1 AAGATTCGCCGTTGTGGCTTCAATCT
59750623 GCTCCACTGC
Statistics
Matches: 137, Mismatches: 31, Indels: 16
0.74 0.17 0.09
Matches are distributed among these distances:
48 1 0.01
49 8 0.06
50 118 0.86
51 10 0.07
ACGTcount: A:0.23, C:0.21, G:0.22, T:0.34
Consensus pattern (48 bp):
AAGATTCGCCGTTGTGGCTTCAATCTTTCTGTTGCACTGCATGGAAGT
Found at i:59750520 original size:100 final size:99
Alignment explanation
Indices: 59750347--59751168 Score: 695
Period size: 100 Copynumber: 8.3 Consensus size: 99
59750337 TTCGTCGAGG
** * * * *** *
59750347 AAGATTCGCCGTTGCGGCCTCAATCTTTTAATTACAATATCGAAAAAAGCAAGATTCGCCGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTAATTGCAATGTC-AGGGAAGTAAGATTCGCCGTTGT
* *** *
59750412 GGCTTCAATCTGTTCTGTTGCACTGCCT-GGAATGT
65 AGCTTCAATCTGTTCCACTGCACTG-CTAGGAAAGT
* * * * *
59750447 AAGATTCACCGTTGTGGCTTCAATCTTTTAAATTACAATGTCAGGGAAGTGAGATTCGCCGTCGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTT-AATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGT
* * * *
59750512 CGCTTCAATCTATTCCGCTGCACTGCTTGGAAAGT
65 AGCTTCAATCTGTTCCACTGCACTGCTAGGAAAGT
* * * * *
59750547 AAGATTCGCCATTGTAGCTTCAATCTTTCTAATTGTAATGTCGGGGAAGCAAGATTCGCCATTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTT-TAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGT
* **
59750612 -GACTTCAATCTGCTCCACTGCAAAGCTAGGAAAGT
65 AG-CTTCAATCTGTTCCACTGCACTGCTAGGAAAGT
* * * * *
59750647 AAGATCCGCTGTTGTAGCCTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATC-TTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGT
59750712 AGCTTCAATCTGTTCCACTGCAAC-GCTAGGAAAGT
65 AGCTTCAATCTGTTCCACTGC-ACTGCTAGGAAAGT
* * * *
59750747 AAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTT-TTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGT
* *
59750812 AGCTTCAATATGTTCCACTGCAAC-ACTAGGAAAGT
65 AGCTTCAATCTGTTCCACTGC-ACTGCTAGGAAAGT
* ** * * ** * *
59750847 AAGATCCGCTATTGTAGCTTCAATC-TTT--TT--AACTGCCGGGGAAACAAGATCCGCTGTTGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTAATTGCAA-TGTCAGGGAAGTAAGATTCGCCGTTGT
** * * *
59750907 AGCTTCAATCT-TCTTAATTGCAATG-TCAGGGAAGT
65 AGCTTCAATCTGT-TCCACTGCACTGCT-AGGAAAGT
* * ** * * * * * **
59750942 AAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACG-CTAAGAAAGTAAGATTTGTTGTTG
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTAATTGCAATGTC-AGGGAAGTAAGATTCGCCGTTG
*
59751006 TAGCTTCAATCTGTTCCACTGCAAC-GCTAGAAAAGT
64 TAGCTTCAATCTGTTCCACTGC-ACTGCTAGGAAAGT
* * * *
59751042 AAGA-TCTGTCGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGAAAGTAAGATCCGCTGTTG
1 AAGATTC-GCCGTTGTAGCTTCAATCTT-TTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTG
*
59751106 TAACTTCAATCTGTTCCACTGCAAC-GCTAGGAAAGT
64 TAGCTTCAATCTGTTCCACTGC-ACTGCTAGGAAAGT
* *
59751142 AAGATCCGCAGTTGTAGCTTC-ATCTTT
1 AAGATTCGCCGTTGTAGCTTCAATCTTT
59751169 CTTAATNNNN
Statistics
Matches: 604, Mismatches: 92, Indels: 54
0.81 0.12 0.07
Matches are distributed among these distances:
94 5 0.01
95 69 0.11
96 2 0.00
97 2 0.00
98 3 0.00
99 15 0.02
100 484 0.80
101 24 0.04
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (99 bp):
AAGATTCGCCGTTGTAGCTTCAATCTTTTAATTGCAATGTCAGGGAAGTAAGATTCGCCGTTGTA
GCTTCAATCTGTTCCACTGCACTGCTAGGAAAGT
Found at i:59750651 original size:50 final size:50
Alignment explanation
Indices: 59750614--59751163 Score: 586
Period size: 50 Copynumber: 11.1 Consensus size: 50
59750604 GCCATTGTGA
* *
59750614 CTTCAATCTGCTCCACTGCAAAGCTAGGAAAGTAAGATCCGCTGTTGTAG
1 CTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAG
* * ** * * *
59750664 CCTCAATCTTTTTAATTGCAATG-TCAGGGAAGTAAGATCCGCTGTTGTAG
1 CTTCAATCTGTTCCACTGCAACGCT-AGGAAAGTAAGATCCGCTGTTGTAG
59750714 CTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAG
1 CTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAG
** * * *
59750764 CTTCAATCT-TCTTAATTGCAATG-TCAGGGAAGTAAGATCCGCTGTTGTAG
1 CTTCAATCTGT-TCCACTGCAACGCT-AGGAAAGTAAGATCCGCTGTTGTAG
* * *
59750814 CTTCAATATGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTATTGTAG
1 CTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAG
* ** * *
59750864 CTTCAATCTTTTTAACTGC--CG--GGGAAA-CAAGATCCGCTGTTGTAG
1 CTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAG
** * * *
59750909 CTTCAATCT-TCTTAATTGCAATG-TCAGGGAAGTAAGATCCGCTGTTGTAG
1 CTTCAATCTGT-TCCACTGCAACGCT-AGGAAAGTAAGATCCGCTGTTGTAG
* ** *
59750959 CTTCAATCTGTTCCACTGCAACGCTAAGAAAGTAAGATTTGTTGTTGTAG
1 CTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAG
* *
59751009 CTTCAATCTGTTCCACTGCAACGCTAGAAAAGTAAGATCTG-TCGTTGTAG
1 CTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCT-GTTGTAG
** * * *
59751059 CTTCAATCT-TCTTAATTGCAATG-TCAGGAAAGTAAGATCCGCTGTTGTAA
1 CTTCAATCTGT-TCCACTGCAACGCT-AGGAAAGTAAGATCCGCTGTTGTAG
*
59751109 CTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCAGTTGTAG
1 CTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAG
59751159 CTTCA
1 CTTCA
59751164 TCTTTCTTAA
Statistics
Matches: 414, Mismatches: 66, Indels: 40
0.80 0.13 0.08
Matches are distributed among these distances:
44 1 0.00
45 32 0.08
46 5 0.01
47 1 0.00
48 1 0.00
49 10 0.02
50 356 0.86
51 8 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (50 bp):
CTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAG
Found at i:59751044 original size:245 final size:245
Alignment explanation
Indices: 59750647--59751117 Score: 673
Period size: 245 Copynumber: 1.9 Consensus size: 245
59750637 CTAGGAAAGT
*
59750647 AAGATCCGCTGTTGTAGCCTCAATCTTTTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGT
1 AAGATCCGCTGTTGTAGCCTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGT
* *
59750712 AGCTTCAATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTT
66 AGCTTCAATCTGTTCCACTGCAACGCTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTC
* * ** *
59750777 AATTGCAATGTCAGGGAAGTAAGATCCG-CTGTTGTAGCTTCAATATGT-TCCACTGCAACACT-
131 AACTGCAACGTCAGAAAAGTAAGATCCGTC-GTTGTAGCTTCAATAT-TCTCAACTGCAA-ACTC
*
59750839 AGGAAAGTAAGATCCGCTATTGTAGCTTCAATCTTTTTAACTGCCGGGGAAAC
193 AGGAAAGTAAGATCCGCTATTGTAACTTCAATCTTTTTAACTGCCGGGGAAAC
*
59750892 AAGATCCGCTGTTGTAGCTTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGT
1 AAGATCCGCTGTTGTAGCCTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGT
** *
59750957 AGCTTCAATCTGTTCCACTGCAACGCTAAGAAAGTAAGATTTGTTGTTGTAGCTTCAATCTGT-T
66 AGCTTCAATCTGTTCCACTGCAACGCTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCT-TCT
* * * * * **
59751021 CCACTGCAACG-CTAGAAAAGTAAGATCTGTCGTTGTAGCTTCAATCTTCTTAATTGCAATGTCA
130 CAACTGCAACGTC-AGAAAAGTAAGATCCGTCGTTGTAGCTTCAATATTCTCAACTGCAAACTCA
*
59751085 GGAAAGTAAGATCCGCTGTTGTAACTTCAATCT
194 GGAAAGTAAGATCCGCTATTGTAACTTCAATCT
59751118 GTTCCACTGC
Statistics
Matches: 200, Mismatches: 21, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
244 3 0.01
245 195 0.98
246 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (245 bp):
AAGATCCGCTGTTGTAGCCTCAATCTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGT
AGCTTCAATCTGTTCCACTGCAACGCTAAGAAAGTAAGATCCGCTGTTGTAGCTTCAATCTTCTC
AACTGCAACGTCAGAAAAGTAAGATCCGTCGTTGTAGCTTCAATATTCTCAACTGCAAACTCAGG
AAAGTAAGATCCGCTATTGTAACTTCAATCTTTTTAACTGCCGGGGAAAC
Found at i:59751171 original size:100 final size:101
Alignment explanation
Indices: 59750457--59751174 Score: 778
Period size: 100 Copynumber: 7.2 Consensus size: 101
59750447 AAGATTCACC
* * * * * * * *
59750457 GTTGTGGCTTCAATCTTT-TAAATTACAATGTCAGGGAAGTGAGATTCGCCGTCGTCGCTTCAAT
1 GTTGTAGCTTCAATCTTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
* * * *
59750521 CTATTCCGCTGC-ACTGCTTGGAAAGTAAGATTCGCCA
66 CTGTTCCACTGCAAC-GCTAGGAAAGTAAGATCCG-CA
* * * * **
59750558 -TTGTAGCTTCAATCTTTC-TAATTGTAATGTCGGGGAAGCAAGATTCGCCATTGT-GACTTCAA
1 GTTGTAGCTTCAATCTTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAG-CTTCAA
* * *
59750620 TCTGCTCCACTGCAAAGCTAGGAAAGTAAGATCCGCT
65 TCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCA
*
59750657 GTTGTAGCCTCAATCTTT-TTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
1 GTTGTAGCTTCAATCTTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
*
59750721 CTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCT
66 CTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCA
59750757 GTTGTAGCTTCAATC-TTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
1 GTTGTAGCTTCAATCTTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
* *
59750821 ATGTTCCACTGCAACACTAGGAAAGTAAGATCCGCTA
66 CTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGC-A
* * **
59750858 -TTGTAGCTTCAATCTTT-TTAA---C--TGCCGGGGAAACAAGATCCGCTGTTGTAGCTTCAAT
1 GTTGTAGCTTCAATCTTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
** * * * *
59750916 CT-TCTTAATTGCAATG-TCAGGGAAGTAAGATCCGCT
66 CTGT-TCCACTGCAACGCT-AGGAAAGTAAGATCCGCA
* * * * * ** *
59750952 GTTGTAGCTTCAATCTGTTC--CACTGCAACG-CTAAGAAAGTAAGATTTGTTGTTGTAGCTTCA
1 GTTGTAGCTTCAATCT-TTCTTAATTGCAATGTC-AGGGAAGTAAGATCCGCTGTTGTAGCTTCA
* *
59751014 ATCTGTTCCACTGCAACGCTAGAAAAGTAAGATCTGTC-
64 ATCTGTTCCACTGCAACGCTAGGAAAGTAAGATCCG-CA
* *
59751052 GTTGTAGCTTCAATC-TTCTTAATTGCAATGTCAGGAAAGTAAGATCCGCTGTTGTAACTTCAAT
1 GTTGTAGCTTCAATCTTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
59751116 CTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCA
66 CTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCA
59751152 GTTGTAGCTTC-ATCTTTCTTAAT
1 GTTGTAGCTTCAATCTTTCTTAAT
59751175 NNNNNNNNNN
Statistics
Matches: 521, Mismatches: 68, Indels: 57
0.81 0.11 0.09
Matches are distributed among these distances:
94 2 0.00
95 72 0.14
96 2 0.00
97 1 0.00
98 4 0.01
99 9 0.02
100 423 0.81
101 8 0.02
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (101 bp):
GTTGTAGCTTCAATCTTTCTTAATTGCAATGTCAGGGAAGTAAGATCCGCTGTTGTAGCTTCAAT
CTGTTCCACTGCAACGCTAGGAAAGTAAGATCCGCA
Found at i:59751410 original size:49 final size:50
Alignment explanation
Indices: 59751275--59751423 Score: 160
Period size: 49 Copynumber: 3.0 Consensus size: 50
59751265 NNNNNNNNNN
*
59751275 TGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCAC
1 TGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCAA
* * * * * * * * *
59751325 CG-CTTGAGAAAGTAAGATTCGCCGTTGTGGCCTCAATCT-TT-TGATTGCAA
1 TGTC-AG-GGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCG-CTGCAA
59751375 TGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCA
1 TGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCA
59751424 CCGCTTGAGA
Statistics
Matches: 74, Mismatches: 19, Indels: 12
0.70 0.18 0.11
Matches are distributed among these distances:
49 29 0.39
50 16 0.22
51 29 0.39
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (50 bp):
TGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCAA
Found at i:59751448 original size:100 final size:101
Alignment explanation
Indices: 59751275--59751475 Score: 386
Period size: 100 Copynumber: 2.0 Consensus size: 101
59751265 NNNNNNNNNN
59751275 TGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAAGTAA
1 TGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAAGTAA
*
59751340 GATTCGCCGTTGTGGCCTCAATCTTTT-GATTGCAA
66 GATTCGCCGTTGTGGCCTCAATCTTTTAAATTGCAA
59751375 TGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAAGTAA
1 TGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAAGTAA
59751440 GATTCGCCGTTGTGGCCTCAATCTTTTAAATTGCAA
66 GATTCGCCGTTGTGGCCTCAATCTTTTAAATTGCAA
59751476 ACTATGGTTA
Statistics
Matches: 99, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
100 92 0.93
101 7 0.07
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.30
Consensus pattern (101 bp):
TGTCAGGGAAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGAAAGTAA
GATTCGCCGTTGTGGCCTCAATCTTTTAAATTGCAA
Found at i:59751451 original size:51 final size:51
Alignment explanation
Indices: 59751283--59751463 Score: 190
Period size: 51 Copynumber: 3.6 Consensus size: 51
59751273 NNTGTCAGGG
* *
59751283 AAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGA
1 AAGTAAGATCCGCCGTTGTAGCCTCAATCTGTTCCGCTGCACCGCTTGAGA
* * * * ** * *
59751334 AAGTAAGATTCGCCGTTGTGGCCTCAATCT-TT-TGATTGCAATG--TCAGGG
1 AAGTAAGATCCGCCGTTGTAGCCTCAATCTGTTCCG-CTGCACCGCTTGA-GA
* *
59751383 AAGTGAGATCCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCTTGAGA
1 AAGTAAGATCCGCCGTTGTAGCCTCAATCTGTTCCGCTGCACCGCTTGAGA
* *
59751434 AAGTAAGATTCGCCGTTGTGGCCTCAATCT
1 AAGTAAGATCCGCCGTTGTAGCCTCAATCT
59751464 TTTAAATTGC
Statistics
Matches: 100, Mismatches: 24, Indels: 12
0.74 0.18 0.09
Matches are distributed among these distances:
48 2 0.02
49 28 0.28
50 14 0.14
51 54 0.54
52 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.25, T:0.29
Consensus pattern (51 bp):
AAGTAAGATCCGCCGTTGTAGCCTCAATCTGTTCCGCTGCACCGCTTGAGA
Found at i:59752646 original size:43 final size:42
Alignment explanation
Indices: 59752557--59752658 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 42
59752547 TGTCCCGATC
* *
59752557 TGATCAAAATTTGAGCTGCTCTGATCGCCTCATCCCCCAATT
1 TGATCAAAATTTGAGCTGCTCTGATCACCTAATCCCCCAATT
* **
59752599 TGATCCAAAATTTGAG-TCGCTCTGATCACTTAATGTCCC-ATT
1 TGAT-CAAAATTTGAGCT-GCTCTGATCACCTAATCCCCCAATT
59752641 ATGATCAAAAGTTTGAGC
1 -TGATCAAAA-TTTGAGC
59752659 CGCCCTTTTC
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
42 13 0.26
43 37 0.74
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (42 bp):
TGATCAAAATTTGAGCTGCTCTGATCACCTAATCCCCCAATT
Found at i:59753895 original size:6 final size:6
Alignment explanation
Indices: 59753884--59753943 Score: 120
Period size: 6 Copynumber: 10.0 Consensus size: 6
59753874 TTAACCTCTC
59753884 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
59753932 ATTTTT ATTTTT
1 ATTTTT ATTTTT
59753944 TCTTGTTTTT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 54 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:59753992 original size:6 final size:6
Alignment explanation
Indices: 59753977--59754010 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
59753967 TACTTCGATT
*
59753977 TTTTTA TTTTTG TTTTTG TTTTTG TTTTTG TTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTT
59754011 GAGTCTGAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.12, T:0.85
Consensus pattern (6 bp):
TTTTTG
Found at i:59758735 original size:26 final size:26
Alignment explanation
Indices: 59758688--59758741 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
59758678 ATTCATAAAA
*
59758688 ATTAAAAACAATATGTACGTATATAT
1 ATTAAAAACAAAATGTACGTATATAT
* *
59758714 ATTAAAAA-AAAATCGTATGTATGTAT
1 ATTAAAAACAAAAT-GTACGTATATAT
59758740 AT
1 AT
59758742 ATATATATAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (26 bp):
ATTAAAAACAAAATGTACGTATATAT
Found at i:59763341 original size:50 final size:50
Alignment explanation
Indices: 59763219--59763507 Score: 303
Period size: 50 Copynumber: 5.7 Consensus size: 50
59763209 AAAGAGATCT
*
59763219 CATGTAAGATCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC--GAGA-C--GAGAGGTCC
*
59763275 CATGTAAGACCATGTCTGGGACATGACATTGGCACCGAGACGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTCC
* *
59763325 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTCC
** * * * ** *
59763375 CCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTCC
* * * * * **
59763425 CATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACATGAAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGACGAGAGGTCC
* * *
59763474 CATGTAAGACCATGACTGGGATATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
59763508 TGTTATTATC
Statistics
Matches: 206, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 127 0.62
52 1 0.00
53 4 0.02
55 2 0.01
56 32 0.16
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGACGAGAGGTCC
Found at i:59763455 original size:150 final size:152
Alignment explanation
Indices: 59763222--59763507 Score: 355
Period size: 149 Copynumber: 1.9 Consensus size: 152
59763212 GAGATCTCAT
* * **
59763222 GTAAGATCATGTCTGGGACATGGCATTGGCATCCTTGAGATCATGAGAGGTCCCATGTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCC-T--GATCATGAGAACTCCCATGTAAGACCA
* * * ** *
59763287 TGTCTGGGACATGACATTGGCACCG-AGACGAGAGGTCCCATGTAAGACCATGTCTGGGACATGG
63 TATCTGGGACATGACATTGGCA--GTACACGAAACATCCCATGTAAGACCATGACTGGGACATGG
59763351 CGTTGGCACCGAGATGAGAGGTCCCCC
126 CGTTGGCACCGAGATGAGAGGTCCCCC
*
59763378 GTAAGACCATGTCTGGGACATGGCATGGGCA-CC-GAT-ATGAGAACTCTCATGTAAGACCATAT
1 GTAAGACCATGTCTGGGACATGGCATGGGCATCCTGATCATGAGAACTCCCATGTAAGACCATAT
* * * * *
59763440 CTGGGATATGGCATTGGCAGTACATGAAACATCCCATGTAAGACCATGACTGGGATATGGCTTTG
66 CTGGGACATGACATTGGCAGTACACGAAACATCCCATGTAAGACCATGACTGGGACATGGCGTTG
59763505 GCA
131 GCA
59763508 TGTTATTATC
Statistics
Matches: 113, Mismatches: 16, Indels: 9
0.82 0.12 0.07
Matches are distributed among these distances:
148 1 0.01
149 39 0.35
150 39 0.35
151 3 0.03
155 2 0.02
156 29 0.26
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (152 bp):
GTAAGACCATGTCTGGGACATGGCATGGGCATCCTGATCATGAGAACTCCCATGTAAGACCATAT
CTGGGACATGACATTGGCAGTACACGAAACATCCCATGTAAGACCATGACTGGGACATGGCGTTG
GCACCGAGATGAGAGGTCCCCC
Found at i:59765088 original size:9 final size:9
Alignment explanation
Indices: 59765069--59765162 Score: 107
Period size: 9 Copynumber: 10.4 Consensus size: 9
59765059 TTTGGTTAAA
*
59765069 AATTAATCG
1 AATTAACCG
*
59765078 AATTACCCG
1 AATTAACCG
59765087 AATTAACCG
1 AATTAACCG
*
59765096 AATTACCCG
1 AATTAACCG
*
59765105 AATTAACTG
1 AATTAACCG
*
59765114 AATTAACCA
1 AATTAACCG
*
59765123 AATTACCCG
1 AATTAACCG
* *
59765132 AACTATCCG
1 AATTAACCG
*
59765141 AATTACCCG
1 AATTAACCG
59765150 AATTAACCG
1 AATTAACCG
59765159 AATT
1 AATT
59765163 GAATCACTAC
Statistics
Matches: 70, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 70 1.00
ACGTcount: A:0.40, C:0.24, G:0.10, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:59770247 original size:12 final size:12
Alignment explanation
Indices: 59770230--59770254 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
59770220 CATTTTTTAA
59770230 AAACTCTAAAAT
1 AAACTCTAAAAT
59770242 AAACTCTAAAAT
1 AAACTCTAAAAT
59770254 A
1 A
59770255 TTTAAATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AAACTCTAAAAT
Found at i:59772743 original size:29 final size:30
Alignment explanation
Indices: 59772710--59772770 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
59772700 ACTTAAATTC
59772710 AACACTTAATTT-TTCAGT-ACTT-ATTTTTT
1 AACACTT-ATTTATTCA-TCACTTAATTTTTT
59772739 AACACTTATTTATTCATCACTTAATTTTTT
1 AACACTTATTTATTCATCACTTAATTTTTT
59772769 AA
1 AA
59772771 TCTATCAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 5 0.17
29 15 0.52
30 9 0.31
ACGTcount: A:0.31, C:0.15, G:0.02, T:0.52
Consensus pattern (30 bp):
AACACTTATTTATTCATCACTTAATTTTTT
Found at i:59774991 original size:19 final size:20
Alignment explanation
Indices: 59774957--59775004 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 20
59774947 AAAATGTTAT
59774957 TAAATTTATCATAAAAGAATA
1 TAAATTTATCATAAAAGAA-A
59774978 TAAATTT-T-ATAAAAGAAA
1 TAAATTTATCATAAAAGAAA
59774996 TCAAATTTA
1 T-AAATTTA
59775005 AAAGTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 2 0.08
19 15 0.60
20 1 0.04
21 7 0.28
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (20 bp):
TAAATTTATCATAAAAGAAA
Found at i:59782390 original size:13 final size:13
Alignment explanation
Indices: 59782372--59782396 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59782362 GCATAACTTT
59782372 TAAAAGTAAAAAC
1 TAAAAGTAAAAAC
59782385 TAAAAGTAAAAA
1 TAAAAGTAAAAA
59782397 AAAAAAGAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.16
Consensus pattern (13 bp):
TAAAAGTAAAAAC
Found at i:59785372 original size:20 final size:21
Alignment explanation
Indices: 59785347--59785389 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
59785337 TGTAGAAGAG
*
59785347 TTGAACC-GATAAAAACTCAA
1 TTGAACCAGATAAAAAATCAA
*
59785367 TTGAACCAGGTAAAAAATCAA
1 TTGAACCAGATAAAAAATCAA
59785388 TT
1 TT
59785390 AAAAACGTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (21 bp):
TTGAACCAGATAAAAAATCAA
Found at i:59787084 original size:34 final size:32
Alignment explanation
Indices: 59787033--59787099 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 32
59787023 TTAATGTGTT
**
59787033 TTTTTGTCACTTAATTATAAAAAAAATCTTTTA
1 TTTTTGTCACCAAATTATAAAAAAAAT-TTTTA
* *
59787066 TTTTTGTCACCAATATTATGAAAAATATTTTTA
1 TTTTTGTCACCAA-ATTATAAAAAAAATTTTTA
59787099 T
1 T
59787100 CACTTAACCG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 17 0.59
34 12 0.41
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.49
Consensus pattern (32 bp):
TTTTTGTCACCAAATTATAAAAAAAATTTTTA
Found at i:59787305 original size:18 final size:19
Alignment explanation
Indices: 59787282--59787319 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
59787272 AAATTTGAAT
59787282 TTTTTAAT-ATAATGTTTA
1 TTTTTAATCATAATGTTTA
*
59787300 TTTTTACTCATAATGTTTA
1 TTTTTAATCATAATGTTTA
59787319 T
1 T
59787320 AAAATTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTAATCATAATGTTTA
Found at i:59788399 original size:2 final size:2
Alignment explanation
Indices: 59788387--59788439 Score: 88
Period size: 2 Copynumber: 26.0 Consensus size: 2
59788377 GATTAACATG
59788387 AT AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
59788430 AT AT AC AT AT
1 AT AT AT AT AT
59788440 TTAAATATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 46 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:59790801 original size:34 final size:34
Alignment explanation
Indices: 59790743--59790823 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
59790733 CTATACTGTG
*
59790743 ATGGGCTAAGGCCTTAATGCATACTGTTACTGAA
1 ATGGGCTAAGGCCTTAATGCATACTGATACTGAA
*
59790777 ATGGGCTAAGGCC-TAACTTG-ATACTGATATTGAA
1 ATGGGCTAAGGCCTTAA--TGCATACTGATACTGAA
* *
59790811 AAGGGCTTAGGCC
1 ATGGGCTAAGGCC
59790824 CAAACCGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 3 0.07
34 36 0.88
35 2 0.05
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.27
Consensus pattern (34 bp):
ATGGGCTAAGGCCTTAATGCATACTGATACTGAA
Found at i:59793409 original size:92 final size:92
Alignment explanation
Indices: 59793258--59793427 Score: 214
Period size: 92 Copynumber: 1.8 Consensus size: 92
59793248 TACCATCATA
* * ** ** ** ** * *
59793258 AAACACATATTGATAGTTCATGTACCATGTTGGGCATTTTCAAAGTTTAGGTACTACATTGGACA
1 AAACACATATTGATAATTCAGGTACCACATTGAACATTTTCAAAGTACAAATACCACATTAGACA
59793323 TTTTATAAAAGTAAAAATACTGTAACG
66 TTTTATAAAAGTAAAAATACTGTAACG
*
59793350 AAACACATATTGATAATTCAGGTACCACATTGAACATTTTCAAAGTACAAATACCACATTAGACC
1 AAACACATATTGATAATTCAGGTACCACATTGAACATTTTCAAAGTACAAATACCACATTAGACA
*
59793415 TTTTATGAAAGTA
66 TTTTATAAAAGTA
59793428 TAACTACCAA
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
92 64 1.00
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.32
Consensus pattern (92 bp):
AAACACATATTGATAATTCAGGTACCACATTGAACATTTTCAAAGTACAAATACCACATTAGACA
TTTTATAAAAGTAAAAATACTGTAACG
Found at i:59798627 original size:16 final size:15
Alignment explanation
Indices: 59798606--59798658 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
59798596 TATATTTCAT
59798606 TTTTTTAACTTTTTTA
1 TTTTTTAA-TTTTTTA
* *
59798622 TTTTTTAA-TTATGA
1 TTTTTTAATTTTTTA
*
59798636 TTTTTTAATTTTATA
1 TTTTTTAATTTTTTA
*
59798651 ATTTTTAA
1 TTTTTTAA
59798659 ATTATTTTTA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 12 0.40
15 10 0.33
16 8 0.27
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTTTTAATTTTTTA
Found at i:59798641 original size:30 final size:30
Alignment explanation
Indices: 59798606--59798663 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
59798596 TATATTTCAT
* *
59798606 TTTTTTAACTTTT-TTATTTTTTAATTATGA
1 TTTTTTAA-TTTTATAATTTTTAAATTATGA
59798636 TTTTTTAATTTTATAATTTTTAAATTAT
1 TTTTTTAATTTTATAATTTTTAAATTAT
59798664 TTTTAACATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (30 bp):
TTTTTTAATTTTATAATTTTTAAATTATGA
Found at i:59803431 original size:3 final size:3
Alignment explanation
Indices: 59803425--59803456 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
59803415 TTCATCATCA
59803425 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
59803457 CATTTTGATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:59807250 original size:3 final size:3
Alignment explanation
Indices: 59807242--59807283 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
59807232 TTCACTAACA
59807242 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
59807284 AGTTTTGGTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:59808364 original size:18 final size:18
Alignment explanation
Indices: 59808341--59808378 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
59808331 TTAACAGTTA
*
59808341 TAGTTAGCTGTTAGCAGT
1 TAGTTAGCTATTAGCAGT
*
59808359 TAGTTAGTTATTAGCAGT
1 TAGTTAGCTATTAGCAGT
59808377 TA
1 TA
59808379 CTGATGTTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.26, C:0.08, G:0.24, T:0.42
Consensus pattern (18 bp):
TAGTTAGCTATTAGCAGT
Found at i:59814236 original size:34 final size:34
Alignment explanation
Indices: 59814197--59814265 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
59814187 TTCATAAATA
59814197 TCAGTTATCCTATGTCAAACAGTAAAGACATAAT
1 TCAGTTATCCTATGTCAAACAGTAAAGACATAAT
59814231 TCAGTTATCCTATGTCAAACAGTAAAGACATAAT
1 TCAGTTATCCTATGTCAAACAGTAAAGACATAAT
59814265 T
1 T
59814266 GCAAGTCTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.30
Consensus pattern (34 bp):
TCAGTTATCCTATGTCAAACAGTAAAGACATAAT
Found at i:59816872 original size:13 final size:14
Alignment explanation
Indices: 59816854--59816888 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
59816844 GGTTTTTAAA
*
59816854 TTTTAAAAATA-GT
1 TTTTAAAAATATAT
59816867 TTTTAAAAATATAT
1 TTTTAAAAATATAT
59816881 TTTTAAAA
1 TTTTAAAA
59816889 TTTTAAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (14 bp):
TTTTAAAAATATAT
Found at i:59818041 original size:17 final size:18
Alignment explanation
Indices: 59818009--59818042 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
59817999 AGGAAATGAT
*
59818009 ATAAAAACAATTAAAATG
1 ATAAAAACAATAAAAATG
59818027 ATAAAAA-AATAAAAAT
1 ATAAAAACAATAAAAAT
59818043 AAAAATTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (18 bp):
ATAAAAACAATAAAAATG
Found at i:59819437 original size:2 final size:2
Alignment explanation
Indices: 59819430--59819459 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59819420 AATGAAAGTT
59819430 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59819460 AGCATAGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59820114 original size:86 final size:86
Alignment explanation
Indices: 59820014--59820288 Score: 272
Period size: 86 Copynumber: 3.2 Consensus size: 86
59820004 AGGAACCTCA
* *
59820014 TTAGAAATTTTGGTATACCAAAATCATGTTGCACAAGCCTATACCAAGATTTTTAATGAAATGCT
1 TTAGAAATTTTGGTATACCAAAATCATGTTACACAAGCCTATACCAAAATTTTTAATGAAATGCT
59820079 AAAATTTCTAAGCGCATATCT
66 AAAATTTCTAAGCGCATATCT
* * ** * * * * * *
59820100 TTAGATATTTTGGTATACCCAAATCGCGTTATAGAAGCTTTTACCAAAATTTCTAA-AAGAATAG
1 TTAGAAATTTTGGTATACCAAAATCATGTTACACAAGCCTATACCAAAATTTTTAATGA-AAT-G
* *
59820164 -TAATATTTCTAAG-G-A-ACCT
64 CTAAAATTTCTAAGCGCATATCT
* *
59820183 TGCTAGAAATTTTGGTATATCAAAATCATGTTACACAAGCCTATACCAAAATTTTCTAGTGAAAT
1 T--TAGAAATTTTGGTATACCAAAATCATGTTACACAAGCCTATACCAAAATTTT-TAATGAAAT
* * * *
59820248 ACCAAAACTTCTAAGCACATATCT
63 GCTAAAATTTCTAAGCGCATATCT
* *
59820272 TTAGATATTTTAGTATA
1 TTAGAAATTTTGGTATA
59820289 TGCTTCAATT
Statistics
Matches: 145, Mismatches: 34, Indels: 19
0.73 0.17 0.10
Matches are distributed among these distances:
83 4 0.03
84 1 0.01
85 44 0.30
86 75 0.52
87 16 0.11
88 1 0.01
89 4 0.03
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.35
Consensus pattern (86 bp):
TTAGAAATTTTGGTATACCAAAATCATGTTACACAAGCCTATACCAAAATTTTTAATGAAATGCT
AAAATTTCTAAGCGCATATCT
Found at i:59835336 original size:23 final size:23
Alignment explanation
Indices: 59835310--59835355 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
59835300 AACGCTTCCT
59835310 TGGGATTCAAAGTGTCTTCACAA
1 TGGGATTCAAAGTGTCTTCACAA
59835333 TGGGATTCAAAGTGTCTTCACAA
1 TGGGATTCAAAGTGTCTTCACAA
59835356 ACCTTCCTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.30
Consensus pattern (23 bp):
TGGGATTCAAAGTGTCTTCACAA
Found at i:59835850 original size:23 final size:23
Alignment explanation
Indices: 59835823--59835896 Score: 64
Period size: 23 Copynumber: 3.3 Consensus size: 23
59835813 ATTAATTATT
59835823 TGAAATTACATTATGTTTATATG
1 TGAAATTACATTATGTTTATATG
* * * *
59835846 TGAAA-TA-TTTCA-ATTAATCATT
1 TGAAATTACATT-ATGTTTAT-ATG
*
59835868 TCAAATTACATTATGTTTATATG
1 TGAAATTACATTATGTTTATATG
59835891 TGAAAT
1 TGAAAT
59835897 ATTTCAATTA
Statistics
Matches: 36, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
21 6 0.17
22 9 0.25
23 15 0.42
24 6 0.17
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (23 bp):
TGAAATTACATTATGTTTATATG
Found at i:59835857 original size:45 final size:45
Alignment explanation
Indices: 59835801--59835948 Score: 269
Period size: 45 Copynumber: 3.3 Consensus size: 45
59835791 TTTTTATACA
*
59835801 TGAAATATTTCAATTAATTATTTGAAATTACATTATGTTTATATG
1 TGAAATATTTCAATTAATTATTTCAAATTACATTATGTTTATATG
*
59835846 TGAAATATTTCAATTAATCATTTCAAATTACATTATGTTTATATG
1 TGAAATATTTCAATTAATTATTTCAAATTACATTATGTTTATATG
59835891 TGAAATATTTCAATTAATTATTTCAAATTACATTATGTTTATATG
1 TGAAATATTTCAATTAATTATTTCAAATTACATTATGTTTATATG
*
59835936 TTAAATATTTCAA
1 TGAAATATTTCAA
59835949 AAAGACGTAC
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 99 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.48
Consensus pattern (45 bp):
TGAAATATTTCAATTAATTATTTCAAATTACATTATGTTTATATG
Found at i:59835914 original size:13 final size:13
Alignment explanation
Indices: 59835806--59835926 Score: 62
Period size: 13 Copynumber: 8.2 Consensus size: 13
59835796 ATACATGAAA
59835806 TATTTCAATTAAT
1 TATTTCAATTAAT
*
59835819 TATTTGAAATTACAT
1 TATTT-CAATTA-AT
* *
59835834 TATGTTTATATGTGAAA
1 TAT-TTCA-AT-T-AAT
59835851 TATTTCAATTAAT
1 TATTTCAATTAAT
*
59835864 CATTTCAAATTACAT
1 TATTTC-AATTA-AT
* *
59835879 TATGTTTATATGTGAAA
1 TAT-TTCA-AT-T-AAT
59835896 TATTTCAATTAAT
1 TATTTCAATTAAT
59835909 TATTTCAAATTACAT
1 TATTTC-AATTA-AT
59835924 TAT
1 TAT
59835927 GTTTATATGT
Statistics
Matches: 83, Mismatches: 11, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
13 20 0.24
14 17 0.20
15 20 0.24
16 14 0.17
17 10 0.12
18 2 0.02
ACGTcount: A:0.38, C:0.07, G:0.06, T:0.49
Consensus pattern (13 bp):
TATTTCAATTAAT
Found at i:59837789 original size:18 final size:18
Alignment explanation
Indices: 59837768--59837910 Score: 96
Period size: 18 Copynumber: 8.0 Consensus size: 18
59837758 AATACGATTT
*
59837768 TTTTTAAAAACACGAGAA
1 TTTTTAAAAACACGAAAA
* *
59837786 -TTTTAGAGACACGAAAA
1 TTTTTAAAAACACGAAAA
* *
59837803 TTCTTAAAAACACGAATA
1 TTTTTAAAAACACGAAAA
*
59837821 TTTTTGAAAACACGACAAA
1 TTTTTAAAAACACGA-AAA
* * *
59837840 TTTTTGAAAACA--ATAT
1 TTTTTAAAAACACGAAAA
** *
59837856 TTTTTTGAAACGCGAAAA
1 TTTTTAAAAACACGAAAA
* *
59837874 TTTTT-GAAACACGAGAAT
1 TTTTTAAAAACACGA-AAA
*
59837892 TTTTTAGAAAACAGGAAAA
1 TTTTTA-AAAACACGAAAA
59837911 AAATAATTTT
Statistics
Matches: 96, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
16 10 0.10
17 23 0.24
18 40 0.42
19 16 0.17
20 7 0.07
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (18 bp):
TTTTTAAAAACACGAAAA
Found at i:59837824 original size:35 final size:37
Alignment explanation
Indices: 59837771--59837851 Score: 96
Period size: 35 Copynumber: 2.2 Consensus size: 37
59837761 ACGATTTTTT
*
59837771 TTAAAAACACGAGAATTTTAG-AGACACGA-AAATTC
1 TTAAAAACACGAGAATTTTAGAAAACACGACAAATTC
* *
59837806 TTAAAAACACGA-ATATTTTTGAAAACACGACAAATTT
1 TTAAAAACACGAGA-ATTTTAGAAAACACGACAAATTC
*
59837843 TTGAAAACA
1 TTAAAAACA
59837852 ATATTTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
34 1 0.03
35 18 0.46
36 7 0.18
37 13 0.33
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (37 bp):
TTAAAAACACGAGAATTTTAGAAAACACGACAAATTC
Found at i:59837877 original size:17 final size:17
Alignment explanation
Indices: 59837775--59838066 Score: 128
Period size: 17 Copynumber: 16.1 Consensus size: 17
59837765 TTTTTTTTAA
* *
59837775 AAACACGAGAATTTTAG
1 AAACACGAAAATTTTTG
* **
59837792 AGACACGAAAATTCTTAA
1 AAACACGAAAATT-TTTG
*
59837810 AAACACGAATATTTTTG
1 AAACACGAAAATTTTTG
59837827 AAAACACGACAAATTTTTG
1 -AAACACGA-AAATTTTTG
*
59837846 AAA-AC-AATATTTTTTTG
1 AAACACGAA-A-ATTTTTG
*
59837863 AAACGCGAAAATTTTTG
1 AAACACGAAAATTTTTG
*
59837880 AAACACGAGAATTTTTTAG
1 AAACACGA-AAATTTTT-G
*
59837899 AAAACAGGAAAAAAATAATTTTTTTTG
1 -AAACACG-----AA-AA---TTTTTG
* *
59837926 -ATCATCG-GAATTTTTG
1 AAACA-CGAAAATTTTTG
59837942 AGAACACGAAAATTTTTG
1 A-AACACGAAAATTTTTG
**
59837960 AAACACCG-GGATTTTTG
1 AAACA-CGAAAATTTTTG
**
59837977 AAAACACGAGGATTTTTG
1 -AAACACGAAAATTTTTG
**
59837995 AAACACGAAAATTTTAA
1 AAACACGAAAATTTTTG
59838012 AAACACGAAAATTTTT-
1 AAACACGAAAATTTTTG
* * *
59838028 AAACAGGGGAATTTTTTCG
1 AAACA-CGAAAATTTTT-G
*
59838047 AAAACACGAAATTTTTTG
1 -AAACACGAAAATTTTTG
59838065 AA
1 AA
59838067 TATTTACAAT
Statistics
Matches: 213, Mismatches: 32, Indels: 60
0.70 0.10 0.20
Matches are distributed among these distances:
15 1 0.00
16 13 0.06
17 90 0.42
18 63 0.30
19 22 0.10
20 11 0.05
24 1 0.00
25 5 0.02
26 1 0.00
27 1 0.00
28 5 0.02
ACGTcount: A:0.43, C:0.11, G:0.14, T:0.31
Consensus pattern (17 bp):
AAACACGAAAATTTTTG
Found at i:59837974 original size:35 final size:34
Alignment explanation
Indices: 59837935--59838066 Score: 140
Period size: 35 Copynumber: 3.8 Consensus size: 34
59837925 GATCATCGGA
*
59837935 ATTTTTGAGAACACGAAAATTTTTGAAACACCGGG
1 ATTTTTGAAAACACGAAAATTTTTGAAACA-CGGG
** **
59837970 ATTTTTGAAAACACGAGGATTTTTGAAACACGAA
1 ATTTTTGAAAACACGAAAATTTTTGAAACACGGG
* * *
59838004 AATTTTAAAAACACGAAAATTTTT-AAACAGGGG
1 ATTTTTGAAAACACGAAAATTTTTGAAACACGGG
*
59838037 AATTTTTTCGAAAACACGAAATTTTTTGAA
1 -A-TTTTT-GAAAACACGAAAATTTTTGAA
59838067 TATTTACAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
33 6 0.08
34 23 0.29
35 31 0.40
36 16 0.21
37 2 0.03
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (34 bp):
ATTTTTGAAAACACGAAAATTTTTGAAACACGGG
Found at i:59838385 original size:10 final size:10
Alignment explanation
Indices: 59838364--59838420 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
59838354 TTAAAACCCG
59838364 TTTTTTC-T-
1 TTTTTTCTTC
59838372 TTTTTTCTTC
1 TTTTTTCTTC
*
59838382 TTTTATCTTC
1 TTTTTTCTTC
* *
59838392 CTTTTTCCTC
1 TTTTTTCTTC
*
59838402 TCTTTTTCTTT
1 T-TTTTTCTTC
59838413 TTTTTTCT
1 TTTTTTCT
59838421 GGACTGGGCT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
8 7 0.18
9 1 0.03
10 23 0.59
11 8 0.21
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:59838417 original size:21 final size:21
Alignment explanation
Indices: 59838371--59838419 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
59838361 CCGTTTTTTC
59838371 TTTTTTT-CTTCTTTTATCTT
1 TTTTTTTCCTTCTTTTATCTT
**
59838391 CCTTTTTCCTCTCTTTT-TCTT
1 TTTTTTTCCT-TCTTTTATCTT
59838412 TTTTTTTC
1 TTTTTTTC
59838420 TGGACTGGGC
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 5 0.22
21 12 0.52
22 6 0.26
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (21 bp):
TTTTTTTCCTTCTTTTATCTT
Found at i:59838469 original size:22 final size:23
Alignment explanation
Indices: 59838441--59838495 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
59838431 GGCCTGTTGG
59838441 GCTGCTGCTAGGCCTGGGGG-CT
1 GCTGCTGCTAGGCCTGGGGGCCT
*
59838463 GCTGCTGCACTGGGCCTGGGGGCCT
1 GCTGCTG--CTAGGCCTGGGGGCCT
59838488 GCTGCTGC
1 GCTGCTGC
59838496 GCTGGGCCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 7 0.24
23 1 0.03
24 12 0.41
25 9 0.31
ACGTcount: A:0.04, C:0.31, G:0.44, T:0.22
Consensus pattern (23 bp):
GCTGCTGCTAGGCCTGGGGGCCT
Found at i:59838469 original size:25 final size:25
Alignment explanation
Indices: 59838441--59838505 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
59838431 GGCCTGTTGG
*
59838441 GCTGCTGCTAGGCCTGGGGG-CTGCT
1 GCTGC-GCTGGGCCTGGGGGCCTGCT
*
59838466 GCTGCACTGGGCCTGGGGGCCTGCT
1 GCTGCGCTGGGCCTGGGGGCCTGCT
59838491 GCTGCGCTGGGCCTG
1 GCTGCGCTGGGCCTG
59838506 CATTTGGGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
24 12 0.33
25 24 0.67
ACGTcount: A:0.03, C:0.31, G:0.45, T:0.22
Consensus pattern (25 bp):
GCTGCGCTGGGCCTGGGGGCCTGCT
Found at i:59838546 original size:24 final size:24
Alignment explanation
Indices: 59838514--59838584 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
59838504 TGCATTTGGG
59838514 CTGCTTCTTTCTTTTTCTTTTTTT
1 CTGCTTCTTTCTTTTTCTTTTTTT
59838538 CTGCTTCTTTCTTTCTT-TCTTTTTT
1 CTGCTTCTTTCTTT-TTCT-TTTTTT
* *
59838563 CTGCTGC-TTCTTTTTCTGTTTT
1 CTGCTTCTTTCTTTTTCTTTTTT
59838585 GGTTTTTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 6 0.14
24 22 0.52
25 14 0.33
ACGTcount: A:0.00, C:0.23, G:0.07, T:0.70
Consensus pattern (24 bp):
CTGCTTCTTTCTTTTTCTTTTTTT
Found at i:59838562 original size:28 final size:28
Alignment explanation
Indices: 59838518--59838575 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
59838508 TTTGGGCTGC
* *
59838518 TTCTTTCTTTTTCTTTTTTTCTGCTTCT
1 TTCTTTCTTTTTCTTTTCTGCTGCTTCT
59838546 TTCTTTCTTTCTT-TTTTCTGCTGCTTCT
1 TTCTTTCTTT-TTCTTTTCTGCTGCTTCT
59838574 TT
1 TT
59838576 TTCTGTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 25 0.93
29 2 0.07
ACGTcount: A:0.00, C:0.22, G:0.05, T:0.72
Consensus pattern (28 bp):
TTCTTTCTTTTTCTTTTCTGCTGCTTCT
Found at i:59838695 original size:7 final size:7
Alignment explanation
Indices: 59838683--59838753 Score: 52
Period size: 7 Copynumber: 9.4 Consensus size: 7
59838673 TTAAAATAAT
59838683 TTTTTTC
1 TTTTTTC
59838690 TTTTTTTC
1 -TTTTTTC
59838698 TTTTTTTC
1 -TTTTTTC
*
59838706 TTCTTTC
1 TTTTTTC
*
59838713 TTCTTCCTC
1 TT-TT-TTC
59838722 TTTTTTTC
1 -TTTTTTC
*
59838730 TTCTTTC
1 TTTTTTC
*
59838737 TTTCTTC
1 TTTTTTC
*
59838744 TTCTTTC
1 TTTTTTC
59838751 TTT
1 TTT
59838754 CTCTTTTTCT
Statistics
Matches: 50, Mismatches: 10, Indels: 7
0.75 0.15 0.10
Matches are distributed among these distances:
7 26 0.52
8 18 0.36
9 4 0.08
10 2 0.04
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTTC
Found at i:59838728 original size:24 final size:24
Alignment explanation
Indices: 59838696--59838767 Score: 103
Period size: 24 Copynumber: 3.0 Consensus size: 24
59838686 TTTCTTTTTT
59838696 TCTTTTTTTCTTCTTTCTTCTTCC
1 TCTTTTTTTCTTCTTTCTTCTTCC
*
59838720 TCTTTTTTTCTTCTTTCTTTCTTCT
1 TCTTTTTTTCTTCTTTC-TTCTTCC
*
59838745 TCTTTCTTTC-TCTTT-TTCTTCC
1 TCTTTTTTTCTTCTTTCTTCTTCC
59838767 T
1 T
59838768 TTCTTTCTTC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
22 7 0.16
24 22 0.50
25 15 0.34
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (24 bp):
TCTTTTTTTCTTCTTTCTTCTTCC
Found at i:59838739 original size:4 final size:4
Alignment explanation
Indices: 59838686--59838776 Score: 77
Period size: 4 Copynumber: 23.5 Consensus size: 4
59838676 AAATAATTTT
* * *
59838686 TTTC TTTT TTTC TTTT TTTC -TTC TTTC -TTC TTCCTC TTTT TTTC -TTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT--TC TTTC TTTC TTTC
*
59838733 TTTC TTTC -TTC -TTC TTTC TTTC TCTT- TTTC TTCC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TT
59838777 CCCCGATCAG
Statistics
Matches: 71, Mismatches: 8, Indels: 16
0.75 0.08 0.17
Matches are distributed among these distances:
3 17 0.24
4 48 0.68
5 2 0.03
6 4 0.06
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTC
Found at i:59838741 original size:35 final size:33
Alignment explanation
Indices: 59838688--59838777 Score: 112
Period size: 35 Copynumber: 2.7 Consensus size: 33
59838678 ATAATTTTTT
*
59838688 TCTTTTT-TTCTTTTTTTCTTCTT-TCTTCTTCCTC
1 TCTTTTTCTTCTTTCTTTCTTCTTCT-TTCTT--TC
*
59838722 TTTTTTTCTTCTTTCTTTCTTCTTCTTTCTTTC
1 TCTTTTTCTTCTTTCTTTCTTCTTCTTTCTTTC
59838755 TCTTTTTCTTCCTTTCTTTCTTC
1 TCTTTTTCTT-CTTTCTTTCTTC
59838778 CCCGATCAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
33 11 0.22
34 18 0.36
35 20 0.40
36 1 0.02
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (33 bp):
TCTTTTTCTTCTTTCTTTCTTCTTCTTTCTTTC
Found at i:59838897 original size:21 final size:22
Alignment explanation
Indices: 59838873--59838916 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
59838863 CCCTTTCCCC
*
59838873 TTTTTTCTCTTTTT-CTTTCTT
1 TTTTTTCTCTTTTTGCTTGCTT
*
59838894 TTTTTTTTCTTTTTGCTTGCTT
1 TTTTTTCTCTTTTTGCTTGCTT
59838916 T
1 T
59838917 GCTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (22 bp):
TTTTTTCTCTTTTTGCTTGCTT
Found at i:59838902 original size:11 final size:11
Alignment explanation
Indices: 59838873--59838907 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
59838863 CCCTTTCCCC
59838873 TTTTTTCTCTTT
1 TTTTTTCT-TTT
*
59838885 TTCTTTCTTTT
1 TTTTTTCTTTT
59838896 TTTTTTCTTTT
1 TTTTTTCTTTT
59838907 T
1 T
59838908 GCTTGCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:59838906 original size:9 final size:9
Alignment explanation
Indices: 59838872--59838934 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
59838862 TCCCTTTCCC
*
59838872 CTTTTTTCT
1 CTTTTTTTT
59838881 CTTTTTCTTT
1 CTTTTT-TTT
59838891 CTTTTTTTT
1 CTTTTTTTT
*
59838900 -TTCTTTTTG
1 CTT-TTTTTT
** *
59838909 CTTGCTTTG
1 CTTTTTTTT
59838918 CTTTTTTTT
1 CTTTTTTTT
59838927 CTTTTTTT
1 CTTTTTTT
59838935 CTTGCCTCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 2 0.05
9 32 0.73
10 10 0.23
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:59838916 original size:26 final size:26
Alignment explanation
Indices: 59838873--59838939 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
59838863 CCCTTTCCCC
* *
59838873 TTTTTTCTCTTTTTCTTTC-TT--TT
1 TTTTTTCTTTTTTTCTTGCTTTGCTT
*
59838896 TTTTTTC-TTTTTGCTTGCTTTGCTT
1 TTTTTTCTTTTTTTCTTGCTTTGCTT
59838921 TTTTTTCTTTTTTTCTTGC
1 TTTTTTCTTTTTTTCTTGC
59838940 CTCTTGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 8 0.22
23 9 0.25
25 9 0.25
26 10 0.28
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (26 bp):
TTTTTTCTTTTTTTCTTGCTTTGCTT
Found at i:59839377 original size:59 final size:60
Alignment explanation
Indices: 59839314--59839427 Score: 176
Period size: 59 Copynumber: 1.9 Consensus size: 60
59839304 AGGGTCCAAA
* *
59839314 TGTAATTTTAAGAAAGTTTAAGGGTCAAAATGTAA-TTTAGAAAAGTTTAGGGGTTGAAC
1 TGTAATTTTAAGAAAGTTTAAGGGTCAAAATGCAATTTTAAAAAAGTTTAGGGGTTGAAC
* * *
59839373 TGTAATTTTGAGAAAGTTTAGGGGTTAAAATGCAATTTTAAAAAAGTTTAGGGGT
1 TGTAATTTTAAGAAAGTTTAAGGGTCAAAATGCAATTTTAAAAAAGTTTAGGGGT
59839428 CAAAATGCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 31 0.63
60 18 0.37
ACGTcount: A:0.38, C:0.03, G:0.25, T:0.35
Consensus pattern (60 bp):
TGTAATTTTAAGAAAGTTTAAGGGTCAAAATGCAATTTTAAAAAAGTTTAGGGGTTGAAC
Found at i:59839437 original size:30 final size:30
Alignment explanation
Indices: 59839286--59839434 Score: 167
Period size: 30 Copynumber: 5.0 Consensus size: 30
59839276 GGCCGAAACA
* * * *
59839286 TAATTTTGAGAAAGTTCAAGGGTCCAAATG
1 TAATTTTAAGAAAGTTTAGGGGTCAAAATG
*
59839316 TAATTTTAAGAAAGTTTAAGGGTCAAAATG
1 TAATTTTAAGAAAGTTTAGGGGTCAAAATG
** *
59839346 TAA-TTT-AGAAAAGTTTAGGGGTTGAACTG
1 TAATTTTAAG-AAAGTTTAGGGGTCAAAATG
* *
59839375 TAATTTTGAGAAAGTTTAGGGGTTAAAATG
1 TAATTTTAAGAAAGTTTAGGGGTCAAAATG
* *
59839405 CAATTTTAAAAAAGTTTAGGGGTCAAAATG
1 TAATTTTAAGAAAGTTTAGGGGTCAAAATG
59839435 CAAAAAAATT
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
28 2 0.02
29 22 0.21
30 77 0.75
31 2 0.02
ACGTcount: A:0.39, C:0.05, G:0.23, T:0.33
Consensus pattern (30 bp):
TAATTTTAAGAAAGTTTAGGGGTCAAAATG
Found at i:59839971 original size:77 final size:76
Alignment explanation
Indices: 59839620--59840373 Score: 992
Period size: 77 Copynumber: 9.8 Consensus size: 76
59839610 AGAAATCGAG
* * * *
59839620 AATAGCTCAGCGTGAAACCCGAGGCCCAACTCACCTCTAGCAATATGAGTTGATTTTTTTG-AAA
1 AATACCTCAGCGTG--ACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGA-TTTTTTGAAAA
* *
59839684 AGCA-AGAATT-GAAA
62 AACAGA-AATTAAAAA
* * * *
59839698 AATACCTC-GACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTGGAAAAA
1 AATACCTCAG-CGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAA
* *
59839760 TAGAAATT-GAAA
64 CAGAAATTAAAAA
* * * * *
59839772 AACACCTC-GACGTGACTCGAGGCTCAACTCACCTCTGGCAATATAAGTTGA-TTTTTG-AAAAA
1 AATACCTCAG-CGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAAA
*
59839834 CAGAAATT--TAA
64 CAGAAATTAAAAA
* *
59839845 AATACCTCAGCGAGAGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTTGATTTTTTGAAAAA
1 AATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTTGATTTTTTGAAAAA
*
59839910 ATAGAAATTAAAAAA
63 ACAGAAATT-AAAAA
*
59839925 AATACCTCAGCGTGACTCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGC
1 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA-C
59839990 AGAAATTAAAAA
65 AGAAATTAAAAA
*
59840002 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAGCA
1 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACA
*
59840067 GAAATTTAAAA
66 GAAATTAAAAA
59840078 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGC
1 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA-C
59840143 AGAAATTAAAAAA
65 AGAAATT-AAAAA
*
59840156 AATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGC
1 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA-C
*
59840221 AGAAATTTAAAA
65 AGAAATTAAAAA
* * *
59840233 AATAACTCAGCGTAACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTTTTGAAAAAAGC
1 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA-C
59840298 AGAAATTAAAAAA
65 AGAAATT-AAAAA
59840311 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
1 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAA
59840374 AAATAGAATT
Statistics
Matches: 622, Mismatches: 38, Indels: 32
0.90 0.05 0.05
Matches are distributed among these distances:
73 15 0.02
74 74 0.12
75 41 0.07
76 114 0.18
77 185 0.30
78 180 0.29
80 13 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (76 bp):
AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAACA
GAAATTAAAAA
Found at i:59840279 original size:155 final size:153
Alignment explanation
Indices: 59839620--59840373 Score: 996
Period size: 155 Copynumber: 4.9 Consensus size: 153
59839610 AGAAATCGAG
* * * * *
59839620 AATAGCTCAGCGTGAAACCCGAGGCCCAACTCACCTCTAGCAATATGAGTTGATTTTTTTG--AA
1 AATACCTCAGCGTG--ACCCGAGGCTCAACTCACCT-TTGTATTATGAGTTGA-TTTTTTGAAAA
* * * *
59839683 AAGCA-AGAATT-GAAAAATACCTC-GACGTGACTCGAGGCTCAACTCACCTCTCGCAATATGAG
62 AAGCAGA-AATTAAAAAAATACCTCAG-CGTGACCCGAGGCTCAACTCACCTCT-GTATTATGAG
* * *
59839745 TTGA--TTTTGGAAAAATAGAAA-TTGAAA
124 TTGATTTTTTGAAAAAACAGAAATTTAAAA
* * * * * *
59839772 AACACCTC-GACGTGACTCGAGGCTCAACTCACCTCTGGCAATATAAGTTGA-TTTTTG-AAAAA
1 AATACCTCAG-CGTGACCCGAGGCTCAACTCACCT-TTGTATTATGAGTTGATTTTTTGAAAAAA
* * *
59839834 -CAGAAATT--TAAAATACCTCAGCGAGAGACCCGAGGCTCAACTCACCTCTCGTAATATGAGTT
64 GCAGAAATTAAAAAAATACCTCAGC--GTGACCCGAGGCTCAACTCACCTCT-GTATTATGAGTT
* *
59839896 GATTTTTTGAAAAAATAGAAATTAAAAAA
126 GATTTTTTGAAAAAACAGAAATT-TAAAA
* *
59839925 AATACCTCAGCGTGACTCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGC
1 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTTTTGAAAAAAGC
59839990 AGAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT
66 AGAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT
*
59840055 TTTGAAAAAGCAGAAATTTAAAA
131 TTTGAAAAAACAGAAATTTAAAA
*
59840078 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTTTTTGAAAAAAGC
1 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTTTTGAAAAAAGC
*
59840143 AGAAATTAAAAAAAATACCTCAGCGTGACCCAAGGCTCAACTCACCTCTGTATTATGAGTTGATT
66 AGAAATT-AAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATT
59840208 TTTTGAAAAAAGCAGAAATTTAAAA
130 TTTTGAAAAAA-CAGAAATTTAAAA
* *
59840233 AATAACTCAGCGTAACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTTTTGAAAAAAGC
1 AATACCTCAGCGTGACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTTTTGAAAAAAGC
59840298 AGAAATTAAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATT
66 AGAAATT-AAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATT
59840363 TTTTGAAAAAA
130 TTTTGAAAAAA
59840374 AAATAGAATT
Statistics
Matches: 552, Mismatches: 32, Indels: 33
0.89 0.05 0.05
Matches are distributed among these distances:
147 11 0.02
148 13 0.02
149 42 0.08
150 33 0.06
151 17 0.03
152 22 0.04
153 115 0.21
154 104 0.19
155 182 0.33
157 13 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (153 bp):
AATACCTCAGCGTGACCCGAGGCTCAACTCACCTTTGTATTATGAGTTGATTTTTTGAAAAAAGC
AGAAATTAAAAAAATACCTCAGCGTGACCCGAGGCTCAACTCACCTCTGTATTATGAGTTGATTT
TTTGAAAAAACAGAAATTTAAAA
Found at i:59841267 original size:11 final size:11
Alignment explanation
Indices: 59841251--59841308 Score: 73
Period size: 11 Copynumber: 5.1 Consensus size: 11
59841241 GATTTTTCTT
59841251 TTTTTGTTTTG
1 TTTTTGTTTTG
59841262 TTTTTGTTTTG
1 TTTTTGTTTTG
59841273 TTCCTTTGTTTTG
1 TT--TTTGTTTTG
59841286 TTATTT-TTTTG
1 TT-TTTGTTTTG
*
59841297 TTTTTTTTTTG
1 TTTTTGTTTTG
59841308 T
1 T
59841309 CTCTCTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
10 3 0.07
11 26 0.60
12 3 0.07
13 11 0.26
ACGTcount: A:0.02, C:0.03, G:0.14, T:0.81
Consensus pattern (11 bp):
TTTTTGTTTTG
Found at i:59841280 original size:24 final size:24
Alignment explanation
Indices: 59841253--59841298 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
59841243 TTTTTCTTTT
59841253 TTTGTTTTGTT-TTTGTTTTGTTCC
1 TTTGTTTTGTTATTT-TTTTGTTCC
59841277 TTTGTTTTGTTATTTTTTTGTT
1 TTTGTTTTGTTATTTTTTTGTT
59841299 TTTTTTTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.02, C:0.04, G:0.15, T:0.78
Consensus pattern (24 bp):
TTTGTTTTGTTATTTTTTTGTTCC
Found at i:59841300 original size:8 final size:8
Alignment explanation
Indices: 59841243--59841303 Score: 52
Period size: 8 Copynumber: 7.6 Consensus size: 8
59841233 TTCATCTTGA
*
59841243 TTTTTCTT
1 TTTTTGTT
59841251 TTTTTGTT
1 TTTTTGTT
59841259 TTGTTT-TT
1 TT-TTTGTT
*
59841267 GTTTTGTT
1 TTTTTGTT
**
59841275 CCTTTGTT
1 TTTTTGTT
* *
59841283 TTGTTATT
1 TTTTTGTT
59841291 TTTTTGTT
1 TTTTTGTT
59841299 TTTTT
1 TTTTT
59841304 TTTGTCTCTC
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
7 3 0.07
8 35 0.85
9 3 0.07
ACGTcount: A:0.02, C:0.05, G:0.11, T:0.82
Consensus pattern (8 bp):
TTTTTGTT
Found at i:59846199 original size:2 final size:2
Alignment explanation
Indices: 59846192--59846216 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59846182 ATAGAAGTTA
59846192 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
59846217 AGCATAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59846846 original size:18 final size:18
Alignment explanation
Indices: 59846825--59846949 Score: 90
Period size: 18 Copynumber: 6.8 Consensus size: 18
59846815 AAAATACGAT
* *
59846825 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* *
59846843 TTTTAG-AGACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
59846860 TTCTTAAAAACACGAATA
1 TTTTTGAAAACACGAAAA
59846878 TTTTTGAAAACACGACAAA
1 TTTTTGAAAACACGA-AAA
** ***
59846897 TTTTTGAAAACAATATTT
1 TTTTTGAAAACACGAAAA
*
59846915 TTTTTGAAAACGTCGAAAAA
1 TTTTTGAAAAC-ACG-AAAA
59846935 TTTTTTGAAAACACG
1 -TTTTTGAAAACACG
59846950 TAGAACTTTT
Statistics
Matches: 78, Mismatches: 24, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
17 12 0.15
18 37 0.47
19 15 0.19
20 3 0.04
21 11 0.14
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:59847455 original size:10 final size:10
Alignment explanation
Indices: 59847434--59847492 Score: 63
Period size: 10 Copynumber: 6.2 Consensus size: 10
59847424 TTAAAACCCG
59847434 TTTTTTC-T-
1 TTTTTTCTTC
59847442 TTTTTTCTTC
1 TTTTTTCTTC
*
59847452 TTTTATCTTC
1 TTTTTTCTTC
*
59847462 TTTTTTCCTC
1 TTTTTTCTTC
59847472 TCTTTTTCTT-
1 T-TTTTTCTTC
59847482 TTTTTT-TTC
1 TTTTTTCTTC
59847491 TT
1 TT
59847493 GACTGGGCTG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
8 9 0.21
9 8 0.19
10 19 0.44
11 7 0.16
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (10 bp):
TTTTTTCTTC
Found at i:59847464 original size:21 final size:20
Alignment explanation
Indices: 59847434--59847492 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 20
59847424 TTAAAACCCG
59847434 TTTT-TTCTTTTTTTCTTCT
1 TTTTCTTCTTTTTTTCTTCT
*
59847453 TTTATCTTCTTTTTTCCTCTCT
1 TTT-TCTTCTTTTTTTCT-TCT
*
59847475 TTTTCTTTTTTTTTTCTT
1 TTTTCTTCTTTTTTTCTT
59847493 GACTGGGCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 3 0.09
20 2 0.06
21 23 0.68
22 6 0.18
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTCTTCTTTTTTTCTTCT
Found at i:59847540 original size:25 final size:25
Alignment explanation
Indices: 59847512--59847562 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
59847502 GGCCTGTTGG
59847512 GCTGCTG--CTAGGCCTGGGGG-CT
1 GCTGCTGCACTAGGCCTGGGGGCCT
*
59847534 GCTGCTGCACTGGGCCTGGGGGCCT
1 GCTGCTGCACTAGGCCTGGGGGCCT
59847559 GCTG
1 GCTG
59847563 GGCCTGCTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 7 0.28
24 12 0.48
25 6 0.24
ACGTcount: A:0.04, C:0.29, G:0.45, T:0.22
Consensus pattern (25 bp):
GCTGCTGCACTAGGCCTGGGGGCCT
Found at i:59847622 original size:23 final size:23
Alignment explanation
Indices: 59847594--59847663 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 23
59847584 TGCATTTGGG
59847594 CTGCTTCTTTCTTCTTCTTTTTT
1 CTGCTTCTTTCTTCTTCTTTTTT
59847617 CTGCTTCTTTCTTTCTTTCTTTTTT
1 CTGCTTCTTTC-TTC-TTCTTTTTT
* * *
59847642 CTGCTGC-TTCTTTTTCTGTTTT
1 CTGCTTCTTTCTTCTTCTTTTTT
59847664 GGTTTTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
22 8 0.19
23 13 0.31
24 6 0.14
25 15 0.36
ACGTcount: A:0.00, C:0.24, G:0.07, T:0.69
Consensus pattern (23 bp):
CTGCTTCTTTCTTCTTCTTTTTT
Found at i:59847648 original size:28 final size:24
Alignment explanation
Indices: 59847593--59847658 Score: 82
Period size: 23 Copynumber: 2.7 Consensus size: 24
59847583 CTGCATTTGG
59847593 GCTGCTTCTTTCTTCTTCTTTTTT
1 GCTGCTTCTTTCTTCTTCTTTTTT
59847617 -CTGCTTCTTTCTTTCTTTCTTTTTTCT
1 GCTGCTTCTTTC-TTC-TTC-TTTTT-T
59847644 GCTGCTTCTTT-TTCT
1 GCTGCTTCTTTCTTCT
59847659 GTTTTGGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
23 11 0.30
24 3 0.08
25 4 0.11
26 8 0.22
27 1 0.03
28 10 0.27
ACGTcount: A:0.00, C:0.26, G:0.08, T:0.67
Consensus pattern (24 bp):
GCTGCTTCTTTCTTCTTCTTTTTT
Found at i:59847789 original size:4 final size:4
Alignment explanation
Indices: 59847770--59847849 Score: 66
Period size: 4 Copynumber: 21.5 Consensus size: 4
59847760 TAATTTTTTT
* * *
59847770 TTTC TTTT TTTC -TTC TTTC -TTC TTCC TCT- TTTC -TTC TTTC TTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
*
59847814 -TTC -TTC TTTC TTTC TCTT- TTTC TTCC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC T-TTC TTTC TTTC TTTC TTTC TT
59847850 CCCCGATCAG
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
3 19 0.31
4 40 0.66
5 2 0.03
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTC
Found at i:59847804 original size:14 final size:14
Alignment explanation
Indices: 59847785--59847851 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
59847775 TTTTTTCTTC
59847785 TTTCTTCTTCCTCT
1 TTTCTTCTTCCTCT
59847799 TTTCTTCTT--TC-
1 TTTCTTCTTCCTCT
*
59847810 TTTCTTCTTCTTTCT
1 TTTCTTCTTC-CTCT
* * *
59847825 TTCTCTTTTTCTTCC
1 TT-TCTTCTTCCTCT
59847840 TTTCTTTCTTCC
1 TTTC-TTCTTCC
59847852 CCGATCAGGC
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
11 9 0.21
12 2 0.05
14 13 0.30
15 12 0.28
16 7 0.16
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTCTTCTTCCTCT
Found at i:59847816 original size:25 final size:26
Alignment explanation
Indices: 59847772--59847837 Score: 84
Period size: 25 Copynumber: 2.6 Consensus size: 26
59847762 ATTTTTTTTT
*
59847772 TCTTTTTTTC-TTCTTTCTTCTTC-C
1 TCTTTTCTTCTTTCTTTCTTCTTCTC
*
59847796 TCTTTTCTTCTTTCTTTCTTCTTCTT
1 TCTTTTCTTCTTTCTTTCTTCTTCTC
59847822 TCTTTCTCTT-TTTCTT
1 TCTTT-TCTTCTTTCTT
59847838 CCTTTCTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 9 0.24
25 13 0.35
26 11 0.30
27 4 0.11
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (26 bp):
TCTTTTCTTCTTTCTTTCTTCTTCTC
Found at i:59847970 original size:21 final size:22
Alignment explanation
Indices: 59847946--59847989 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
59847936 CCCTTTCCCC
*
59847946 TTTTTTCTCTTTTT-CTTTCTT
1 TTTTTTCTCTTTTTGCTTGCTT
*
59847967 TTTTTTTTCTTTTTGCTTGCTT
1 TTTTTTCTCTTTTTGCTTGCTT
59847989 T
1 T
59847990 GCTTTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.80
Consensus pattern (22 bp):
TTTTTTCTCTTTTTGCTTGCTT
Found at i:59847975 original size:11 final size:11
Alignment explanation
Indices: 59847946--59847980 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
59847936 CCCTTTCCCC
59847946 TTTTTTCTCTTT
1 TTTTTTCT-TTT
*
59847958 TTCTTTCTTTT
1 TTTTTTCTTTT
59847969 TTTTTTCTTTT
1 TTTTTTCTTTT
59847980 T
1 T
59847981 GCTTGCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:59847979 original size:9 final size:9
Alignment explanation
Indices: 59847945--59848007 Score: 56
Period size: 9 Copynumber: 6.9 Consensus size: 9
59847935 TCCCTTTCCC
*
59847945 CTTTTTTCT
1 CTTTTTTTT
59847954 CTTTTTCTTT
1 CTTTTT-TTT
59847964 CTTTTTTTT
1 CTTTTTTTT
*
59847973 -TTCTTTTTG
1 CTT-TTTTTT
** *
59847982 CTTGCTTTG
1 CTTTTTTTT
59847991 CTTTTTTTT
1 CTTTTTTTT
59848000 CTTTTTTT
1 CTTTTTTT
59848008 CTTGCCTCTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
8 2 0.05
9 32 0.73
10 10 0.23
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.79
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:59847989 original size:26 final size:26
Alignment explanation
Indices: 59847946--59848012 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
59847936 CCCTTTCCCC
* *
59847946 TTTTTTCTCTTTTTCTTTC-TT--TT
1 TTTTTTCTTTTTTTCTTGCTTTGCTT
*
59847969 TTTTTTC-TTTTTGCTTGCTTTGCTT
1 TTTTTTCTTTTTTTCTTGCTTTGCTT
59847994 TTTTTTCTTTTTTTCTTGC
1 TTTTTTCTTTTTTTCTTGC
59848013 CTCTTGGTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 8 0.22
23 9 0.25
25 9 0.25
26 10 0.28
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (26 bp):
TTTTTTCTTTTTTTCTTGCTTTGCTT
Found at i:59848452 original size:59 final size:60
Alignment explanation
Indices: 59848389--59848502 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 60
59848379 AGGGTCCAAA
**
59848389 TGTAATGTTAAGAAAGTTTAGGGGTCAAAATGTAA-TTTAGAAAAGTTTAGGGGTTGAAC
1 TGTAATGTTAAGAAAGTTTAGGGGTCAAAATACAATTTTAGAAAAGTTTAGGGGTTGAAC
* * * *
59848448 TGTAATTTTGAGAAATTTTAGGGGTTAAAATACAATTTTAGAAAAGTTTAGGGGT
1 TGTAATGTTAAGAAAGTTTAGGGGTCAAAATACAATTTTAGAAAAGTTTAGGGGT
59848503 CAAAATGCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 29 0.60
60 19 0.40
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (60 bp):
TGTAATGTTAAGAAAGTTTAGGGGTCAAAATACAATTTTAGAAAAGTTTAGGGGTTGAAC
Found at i:59848470 original size:30 final size:30
Alignment explanation
Indices: 59848360--59848509 Score: 160
Period size: 30 Copynumber: 5.0 Consensus size: 30
59848350 GGGCCGAAAC
* * *
59848360 GTAATTTTGAGAAAGTTCAAGGGTCCAAAT
1 GTAATTTTGAGAAAGTTTAGGGGTCAAAAT
* *
59848390 GTAATGTTAAGAAAGTTTAGGGGTCAAAAT
1 GTAATTTTGAGAAAGTTTAGGGGTCAAAAT
* ** *
59848420 GTAATTTAGA-AAAGTTTAGGGGTTGAACT
1 GTAATTTTGAGAAAGTTTAGGGGTCAAAAT
* *
59848449 GTAATTTTGAGAAATTTTAGGGGTTAAAAT
1 GTAATTTTGAGAAAGTTTAGGGGTCAAAAT
**
59848479 ACAATTTT-AGAAAAGTTTAGGGGTCAAAAT
1 GTAATTTTGAG-AAAGTTTAGGGGTCAAAAT
59848509 G
1 G
59848510 CAAAAAAAAT
Statistics
Matches: 98, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
29 27 0.28
30 71 0.72
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.33
Consensus pattern (30 bp):
GTAATTTTGAGAAAGTTTAGGGGTCAAAAT
Found at i:59851595 original size:13 final size:13
Alignment explanation
Indices: 59851543--59851595 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
59851533 TTTAAGCCAA
59851543 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
**
59851556 ACTCCTCAAAAGC
1 ACTTTTCAAAAGC
* *
59851569 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
59851582 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
59851595 A
1 A
59851596 ATGAAGAACT
Statistics
Matches: 31, Mismatches: 9, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.36, C:0.28, G:0.08, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:59852806 original size:2 final size:2
Alignment explanation
Indices: 59852799--59852827 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59852789 ACCAAAACAA
59852799 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59852828 AAAATTCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59853890 original size:31 final size:31
Alignment explanation
Indices: 59853832--59853899 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
59853822 TTAATAACTT
*
59853832 AGTGACTTAAATAAAAACTCTTGAATAGTTC
1 AGTGACTTAAATAAAAACTCTTAAATAGTTC
* *
59853863 AGTGACTTAAATGAAAA-TTTTAAAATAGTTC
1 AGTGACTTAAATAAAAACTCTT-AAATAGTTC
*
59853894 AATGAC
1 AGTGAC
59853900 CAAATTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 3 0.09
31 29 0.91
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (31 bp):
AGTGACTTAAATAAAAACTCTTAAATAGTTC
Found at i:59866212 original size:9 final size:9
Alignment explanation
Indices: 59866198--59866429 Score: 63
Period size: 9 Copynumber: 25.3 Consensus size: 9
59866188 GGAATCATAC
59866198 AAATTATAA
1 AAATTATAA
*
59866207 AAATTA-CA
1 AAATTATAA
* *
59866215 AAATAATTA
1 AAATTATAA
59866224 AAA-TACTAA
1 AAATTA-TAA
*
59866233 AAATTAAAA
1 AAATTATAA
*
59866242 AAACTATAA
1 AAATTATAA
* * *
59866251 AAGTGAAAA
1 AAATTATAA
59866260 AAATTATAA
1 AAATTATAA
* *
59866269 AAATCATTAT
1 AAATTA-TAA
*
59866279 AAATGACTCAA
1 AAATTA-T-AA
*
59866290 AAACTATAA
1 AAATTATAA
*
59866299 AAATTATTA
1 AAATTATAA
*
59866308 TAA-TA-AA
1 AAATTATAA
59866315 AAATT-TAA
1 AAATTATAA
* *
59866323 AATTTTATAT
1 AA-ATTATAA
*
59866333 GAATTA-AA
1 AAATTATAA
59866341 AAA--ATAA
1 AAATTATAA
*
59866348 AAATATATATGG
1 AAAT-TATA--A
* *
59866360 AAATTTTTA
1 AAATTATAA
59866369 AAA-TATAAA
1 AAATTAT-AA
59866378 AAATTATTAA
1 AAATTA-TAA
59866388 AATTATTATAA
1 AA--ATTATAA
59866399 AAA-TATAGA
1 AAATTATA-A
*
59866408 AAAGTGCA-AA
1 AAA-T-TATAA
59866418 AAATTATAA
1 AAATTATAA
59866427 AAA
1 AAA
59866430 AAATTATTAC
Statistics
Matches: 157, Mismatches: 41, Indels: 50
0.63 0.17 0.20
Matches are distributed among these distances:
6 1 0.01
7 8 0.05
8 24 0.15
9 74 0.47
10 27 0.17
11 14 0.09
12 9 0.06
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.30
Consensus pattern (9 bp):
AAATTATAA
Found at i:59866480 original size:18 final size:17
Alignment explanation
Indices: 59866450--59866486 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
59866440 AAAATTTTCA
59866450 AAATAATAGAAAATTAC
1 AAATAATAGAAAATTAC
*
59866467 AAATATATATAAAATTAC
1 AAATA-ATAGAAAATTAC
59866485 AA
1 AA
59866487 TAAGGAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (17 bp):
AAATAATAGAAAATTAC
Found at i:59866702 original size:9 final size:9
Alignment explanation
Indices: 59866690--59866794 Score: 58
Period size: 9 Copynumber: 11.6 Consensus size: 9
59866680 GAAAAAAATG
59866690 TTTTTTATA
1 TTTTTTATA
59866699 -TTTTTAGT-
1 TTTTTTA-TA
59866707 TTGTTTTATA
1 TT-TTTTATA
*
59866717 ATTTTTATGA
1 TTTTTTAT-A
59866727 TTTTTATATTA
1 TTTTT-TA-TA
* *
59866738 TTTTGTAAA
1 TTTTTTATA
59866747 TTTTATTAT-
1 TTTT-TTATA
**
59866756 TTTTAAATA
1 TTTTTTATA
*
59866765 TTTTTCATA
1 TTTTTTATA
*
59866774 ATTTTTA-A
1 TTTTTTATA
59866782 TTTTTTA-A
1 TTTTTTATA
59866790 TTTTT
1 TTTTT
59866795 GTAATTCATT
Statistics
Matches: 74, Mismatches: 13, Indels: 19
0.70 0.12 0.18
Matches are distributed among these distances:
8 21 0.28
9 30 0.41
10 15 0.20
11 7 0.09
12 1 0.01
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.70
Consensus pattern (9 bp):
TTTTTTATA
Found at i:59866730 original size:28 final size:27
Alignment explanation
Indices: 59866691--59866786 Score: 90
Period size: 28 Copynumber: 3.5 Consensus size: 27
59866681 AAAAAAATGT
*
59866691 TTTTTATATTTTTAGT-TTGTTTTATAA
1 TTTTTATATTTTTA-TATTATTTTATAA
*
59866718 TTTTTATGATTTTTATATTATTTTGTAA
1 TTTTTAT-ATTTTTATATTATTTTATAA
* *
59866746 ATTTTATTATTTTTAAATATT-TTTCATAA
1 TTTTTA-TATTTTT--ATATTATTTTATAA
59866775 TTTTTA-ATTTTT
1 TTTTTATATTTTT
59866787 TAATTTTTGT
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
27 14 0.24
28 27 0.47
29 12 0.21
30 5 0.09
ACGTcount: A:0.26, C:0.01, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTTTATATTTTTATATTATTTTATAA
Found at i:59866799 original size:9 final size:8
Alignment explanation
Indices: 59866775--59866813 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
59866765 TTTTTCATAA
59866775 TTTTTAAT
1 TTTTTAAT
59866783 TTTTTAAT
1 TTTTTAAT
59866791 TTTTGTAAT
1 TTTT-TAAT
*
59866800 TCATTTAAT
1 T-TTTTAAT
59866809 TTTTT
1 TTTTT
59866814 CTATATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 15 0.56
9 10 0.37
10 2 0.07
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (8 bp):
TTTTTAAT
Found at i:59870068 original size:13 final size:12
Alignment explanation
Indices: 59870040--59870073 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
59870030 CGTATTAAAG
59870040 TTTTTTATATTA
1 TTTTTTATATTA
*
59870052 TTTTATATATATA
1 TTTTTTATAT-TA
59870065 TTTTTTATA
1 TTTTTTATA
59870074 AAAAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 9 0.47
13 10 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTTATATTA
Found at i:59870267 original size:11 final size:11
Alignment explanation
Indices: 59870253--59870288 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
59870243 ATATACAACC
*
59870253 AATAATAGTAA
1 AATAATAGCAA
59870264 AATAATAGCAA
1 AATAATAGCAA
*
59870275 CATAATAGCAA
1 AATAATAGCAA
59870286 AAT
1 AAT
59870289 GGTAACAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.22
Consensus pattern (11 bp):
AATAATAGCAA
Found at i:59870948 original size:41 final size:41
Alignment explanation
Indices: 59870829--59870948 Score: 161
Period size: 41 Copynumber: 2.9 Consensus size: 41
59870819 TGCCGCTAAT
* * * *
59870829 AGAAAAAAGCCGCAATAGGTAAAGTAGTAGCAGCGTTTATG
1 AGAAAAACGCCGCAAAAGGTCAAGCAGTAGCAGCGTTTATG
* *
59870870 AGAAAAACGCCGCAAAATGTCAAGCAGTAAC-GACGTTTATG
1 AGAAAAACGCCGCAAAAGGTCAAGCAGTAGCAG-CGTTTATG
*
59870911 AGAAAAACGCCGCAAAAGGTCAAGCAATAGCAGCGTTT
1 AGAAAAACGCCGCAAAAGGTCAAGCAGTAGCAGCGTTT
59870949 TTACAAACAC
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 1 0.01
41 66 0.97
42 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (41 bp):
AGAAAAACGCCGCAAAAGGTCAAGCAGTAGCAGCGTTTATG
Found at i:59871075 original size:14 final size:14
Alignment explanation
Indices: 59871056--59871085 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59871046 ATCCTTTTTT
59871056 TCCCCAAATCAAAA
1 TCCCCAAATCAAAA
*
59871070 TCCCCAAATCGAAA
1 TCCCCAAATCAAAA
59871084 TC
1 TC
59871086 TCAAAATCCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.37, G:0.03, T:0.17
Consensus pattern (14 bp):
TCCCCAAATCAAAA
Found at i:59871201 original size:25 final size:25
Alignment explanation
Indices: 59871147--59871206 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 25
59871137 CCTCTATGTT
*
59871147 GCATCGTCGTCGACACTCCTCTGCC
1 GCATCGCCGTCGACACTCCTCTGCC
* * *
59871172 ACATCGCCGTTGACACTCCTCTGTC
1 GCATCGCCGTCGACACTCCTCTGCC
*
59871197 GCATCACCGT
1 GCATCGCCGT
59871207 GTAAGTTTTT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.15, C:0.42, G:0.18, T:0.25
Consensus pattern (25 bp):
GCATCGCCGTCGACACTCCTCTGCC
Found at i:59871844 original size:28 final size:28
Alignment explanation
Indices: 59871813--59871871 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
59871803 ATATTGGTAC
*
59871813 TTGCAATTAACTTGGAAAATATAAAATT
1 TTGCAATTAACTTGGAAAATATAAAAAT
*
59871841 TTGCATTTAACTTGGAAAATATAAAAAT
1 TTGCAATTAACTTGGAAAATATAAAAAT
59871869 TTG
1 TTG
59871872 GAGATTTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.12, T:0.37
Consensus pattern (28 bp):
TTGCAATTAACTTGGAAAATATAAAAAT
Found at i:59874010 original size:21 final size:21
Alignment explanation
Indices: 59873984--59874158 Score: 192
Period size: 21 Copynumber: 8.3 Consensus size: 21
59873974 GTACATTGTT
59873984 AACAGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
*
59874005 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* * *
59874026 AATAGAAACTCATAAGAGTTG
1 AACAGAAGCTCATAAGAGCTG
* *
59874047 AACAGAAGCTCGTAAGAGCTT
1 AACAGAAGCTCATAAGAGCTG
* * * *
59874068 AACAAAAACTCATAACAGTTG
1 AACAGAAGCTCATAAGAGCTG
59874089 AACAGAAGCTCGA-AAGAGCTG
1 AACAGAAGCTC-ATAAGAGCTG
* *
59874110 AATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTG
* *
59874131 AACAG-AGAATCGTAAGAGCTG
1 AACAGAAG-CTCATAAGAGCTG
59874152 AACAGAA
1 AACAGAA
59874159 AGTAAAACAC
Statistics
Matches: 126, Mismatches: 24, Indels: 7
0.80 0.15 0.04
Matches are distributed among these distances:
20 2 0.02
21 122 0.97
22 2 0.02
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTG
Found at i:59874051 original size:42 final size:42
Alignment explanation
Indices: 59873984--59874159 Score: 228
Period size: 42 Copynumber: 4.2 Consensus size: 42
59873974 GTACATTGTT
*
59873984 AACAGAAGCTCATAAGAGCTGAACAGAAGCTCGTAAGAGCTG
1 AACAGAAACTCATAAGAGCTGAACAGAAGCTCGTAAGAGCTG
* * *
59874026 AATAGAAACTCATAAGAGTTGAACAGAAGCTCGTAAGAGCTT
1 AACAGAAACTCATAAGAGCTGAACAGAAGCTCGTAAGAGCTG
* * * *
59874068 AACAAAAACTCATAACAGTTGAACAGAAGCTCGAAAGAGCTG
1 AACAGAAACTCATAAGAGCTGAACAGAAGCTCGTAAGAGCTG
* * * *
59874110 AATAGAAGCTCGTAAGAGCTGAACAG-AGAATCGTAAGAGCTG
1 AACAGAAACTCATAAGAGCTGAACAGAAG-CTCGTAAGAGCTG
59874152 AACAGAAA
1 AACAGAAA
59874160 GTAAAACACG
Statistics
Matches: 114, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
41 2 0.02
42 112 0.98
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.16
Consensus pattern (42 bp):
AACAGAAACTCATAAGAGCTGAACAGAAGCTCGTAAGAGCTG
Found at i:59875834 original size:43 final size:42
Alignment explanation
Indices: 59875753--59876011 Score: 250
Period size: 43 Copynumber: 6.0 Consensus size: 42
59875743 TAACATGACT
**
59875753 TTTAGCGGCGTTTTTTGGGAAAAGCATCGCTAAAGGTCATGTTC
1 TTTAGCGGCG-TTTTTGGG-AAAGCGCCGCTAAAGGTCATGTTC
* * *
59875797 TTTAGTGGCGTTTGTTGGGAAAGCGCCGCTAAAGGTCATATTG
1 TTTAGCGGCGTTT-TTGGGAAAGCGCCGCTAAAGGTCATGTTC
* * * ** * *
59875840 TTTAGTGGCATTTGTGGGGAAAGCATCACTAAAGGCCATGTTC
1 TTTAGCGGCGTTT-TTGGGAAAGCGCCGCTAAAGGTCATGTTC
* * * *
59875883 TTTAGCAGCATTTATGGGGAAAACGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTT-TTGGGAAAGCGCCGCTAAAGGTCATGTTC
* *
59875926 TATAGCGGTGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGTTC
1 TTTAGCGGCGTTTTT-GGGAAAGCGCCGCTAAAGGTCATGTTC
* * * *
59875969 -TTAGCGGCGTTTTTGAGAAAAGCGCTGTTAAAAGTCATGTTC
1 TTTAGCGGCGTTTTTG-GGAAAGCGCCGCTAAAGGTCATGTTC
59876011 T
1 T
59876012 AAAAAAAGCA
Statistics
Matches: 178, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
41 1 0.01
42 35 0.20
43 128 0.72
44 14 0.08
ACGTcount: A:0.24, C:0.16, G:0.29, T:0.32
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAAAGGTCATGTTC
Found at i:59885772 original size:3 final size:3
Alignment explanation
Indices: 59885764--59885789 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
59885754 TACCAAGCAA
59885764 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
59885790 GTTGACATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:59888892 original size:29 final size:28
Alignment explanation
Indices: 59888859--59888919 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
59888849 AAAAGCCACT
59888859 TTTTTTAAAAAATTACCGAAATGGGCCAA
1 TTTTTTAAAAAATTACCGAAATGGGCC-A
** * *
59888888 TTTTTTAATTATTTACCGGAATGGGCCA
1 TTTTTTAAAAAATTACCGAAATGGGCCA
59888916 TTTT
1 TTTT
59888920 CCCCGAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (28 bp):
TTTTTTAAAAAATTACCGAAATGGGCCA
Found at i:59889406 original size:24 final size:22
Alignment explanation
Indices: 59889327--59889396 Score: 97
Period size: 22 Copynumber: 3.2 Consensus size: 22
59889317 ATTTGAGAGT
*
59889327 TTGAGAGAA-TTTTGAAAGAAAA
1 TTGAGAGAATTTTTG-AAGGAAA
*
59889349 TTGAGAGAATTTTTGAAGGGAA
1 TTGAGAGAATTTTTGAAGGAAA
*
59889371 TTGAGAGAATTTTTTAAGGAAA
1 TTGAGAGAATTTTTGAAGGAAA
59889393 TTGA
1 TTGA
59889397 TATTGAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 38 0.88
23 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.26, T:0.33
Consensus pattern (22 bp):
TTGAGAGAATTTTTGAAGGAAA
Found at i:59892155 original size:2 final size:2
Alignment explanation
Indices: 59892148--59892176 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59892138 TCATAAACTA
59892148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59892177 AGGGTGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59892297 original size:3 final size:3
Alignment explanation
Indices: 59892289--59892348 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
59892279 TAAATGAGTA
* * *
59892289 AAT AAT AAT AAT GAT GAT AAT AAT AAT -AT AAT -AT AAT AGT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
59892335 AAT ATT AA- AAT AAT
1 AAT AAT AAT AAT AAT
59892349 TAATTTAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
2 6 0.12
3 42 0.88
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:59898382 original size:33 final size:33
Alignment explanation
Indices: 59898266--59898416 Score: 162
Period size: 33 Copynumber: 4.5 Consensus size: 33
59898256 TACTTTCTTT
* *
59898266 TTGGTGTGATGGTTGGTTTTGCTCTTATAAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATAAGCA
* *
59898299 TTGGTGTGATGG-TCGATTTAGCTCTTATGAGCA
1 TTGGTGTGATGGTTGGA-TTAGCTCTTATAAGCA
*
59898332 TTGGTATGATGGTTGGATTAGCTCTTATAAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTATAAGCA
* * * *
59898365 TTGATGTGATGGATGGATTGGCTC-GAGTAAGCA
1 TTGGTGTGATGGTTGGATTAGCTCTTA-TAAGCA
*
59898398 TCTGGTGTGTTGGGTTGGA
1 T-TGGTGTGAT-GGTTGGA
59898417 CTGATGATGT
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
32 3 0.03
33 79 0.81
34 10 0.10
35 6 0.06
ACGTcount: A:0.19, C:0.09, G:0.33, T:0.39
Consensus pattern (33 bp):
TTGGTGTGATGGTTGGATTAGCTCTTATAAGCA
Found at i:59899947 original size:22 final size:24
Alignment explanation
Indices: 59899914--59899958 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
59899904 TCATGAGTTT
*
59899914 TTCTAAAAATAAACTA-AGTTTTC
1 TTCTAAAAATAAACAATAGTTTTC
59899937 TTCT-AAAATAAACAATAGTTTT
1 TTCTAAAAATAAACAATAGTTTT
59899959 AAAATGACTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (24 bp):
TTCTAAAAATAAACAATAGTTTTC
Found at i:59902725 original size:13 final size:14
Alignment explanation
Indices: 59902702--59902729 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
59902692 TAATAGAATC
59902702 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
59902716 TTTCTTTTTTTTTT
1 TTTCTTTTTTTTTT
59902730 GCTTTGTGCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (14 bp):
TTTCTTTTTTTTTT
Found at i:59914227 original size:21 final size:22
Alignment explanation
Indices: 59914202--59914244 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
59914192 CAGACTGACT
59914202 AATAAAATTATA-AAAATAAAA
1 AATAAAATTATACAAAATAAAA
59914223 AATAAAATTATACAAAATAAAA
1 AATAAAATTATACAAAATAAAA
59914245 TAAAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
AATAAAATTATACAAAATAAAA
Found at i:59919747 original size:28 final size:28
Alignment explanation
Indices: 59919690--59919749 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
59919680 GATTTCCCGG
*
59919690 AAAATGGCCCATTCCGATAAATAATCAA
1 AAAATGGCCCATTCCGATAAATAATAAA
* * *
59919718 AAAATCGGCCCATTTCGGTAAAT-TTAAA
1 AAAAT-GGCCCATTCCGATAAATAATAAA
59919746 AAAA
1 AAAA
59919750 AACAGCTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 12 0.44
29 15 0.56
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (28 bp):
AAAATGGCCCATTCCGATAAATAATAAA
Found at i:59924250 original size:32 final size:32
Alignment explanation
Indices: 59924214--59924278 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
59924204 TTATTAAAAA
59924214 TTTATATAAAAATCAATTATTATTTTAATTAC
1 TTTATATAAAAATCAATTATTATTTTAATTAC
59924246 TTTATATAAAAATCAATTATTATTTTAATTAC
1 TTTATATAAAAATCAATTATTATTTTAATTAC
59924278 T
1 T
59924279 ATGGTAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (32 bp):
TTTATATAAAAATCAATTATTATTTTAATTAC
Found at i:59925062 original size:24 final size:23
Alignment explanation
Indices: 59925035--59925083 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
59925025 AAACTGAAGT
59925035 AAAAAAAAG-TTGGCATGTTGAAAA
1 AAAAAAAAGCTT-GCATGTT-AAAA
*
59925059 AAAATAAAGCTTGCATGTTAAAA
1 AAAAAAAAGCTTGCATGTTAAAA
59925082 AA
1 AA
59925084 GTACGGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
24 15 0.65
25 2 0.09
ACGTcount: A:0.55, C:0.06, G:0.16, T:0.22
Consensus pattern (23 bp):
AAAAAAAAGCTTGCATGTTAAAA
Done.